HEADER VIRAL PROTEIN/IMMUNE SYSTEM 24-APR-21 7MKM TITLE SARS-COV-2 SPIKE RBD IN COMPLEX WITH NEUTRALIZING FAB SARS2-38 (LOCAL TITLE 2 REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN (UNP RESIDUES 333-520); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SARS2-38 FV HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SARS2-38 FV LIGHT CHAIN; COMPND 11 CHAIN: L SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: EXPI293F; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 16 ORGANISM_TAXID: 10090 KEYWDS GLYCOPROTEIN, ANTIBODY, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX, KEYWDS 2 STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS KEYWDS 3 DISEASES, CSGID EXPDTA ELECTRON MICROSCOPY AUTHOR L.J.ADAMS,D.H.FREMONT,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS AUTHOR 2 DISEASES (CSGID) REVDAT 3 01-DEC-21 7MKM 1 JRNL REVDAT 2 04-AUG-21 7MKM 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQRES HELIX SHEET SSBOND REVDAT 2 3 1 LINK ATOM REVDAT 1 12-MAY-21 7MKM 0 JRNL AUTH L.A.VANBLARGAN,L.J.ADAMS,Z.LIU,R.E.CHEN,P.GILCHUK,S.RAJU, JRNL AUTH 2 B.K.SMITH,H.ZHAO,J.B.CASE,E.S.WINKLER,B.M.WHITENER,L.DROIT, JRNL AUTH 3 I.D.AZIATI,T.L.BRICKER,A.JOSHI,P.Y.SHI,A.CREANGA,A.PEGU, JRNL AUTH 4 S.A.HANDLEY,D.WANG,A.C.M.BOON,J.E.CROWE JR.,S.P.J.WHELAN, JRNL AUTH 5 D.H.FREMONT,M.S.DIAMOND JRNL TITL A POTENTLY NEUTRALIZING SARS-COV-2 ANTIBODY INHIBITS JRNL TITL 2 VARIANTS OF CONCERN BY UTILIZING UNIQUE BINDING RESIDUES IN JRNL TITL 3 A HIGHLY CONSERVED EPITOPE. JRNL REF IMMUNITY V. 54 2399 2021 JRNL REFN ISSN 1074-7613 JRNL PMID 34481543 JRNL DOI 10.1016/J.IMMUNI.2021.08.016 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.VANBLARGAN,L.ADAMS,Z.LIU,R.E.CHEN,P.GILCHUK,S.RAJU, REMARK 1 AUTH 2 B.SMITH,H.ZHAO,J.B.CASE,E.S.WINKLER,B.WHITENER,L.DROIT, REMARK 1 AUTH 3 I.AZIATI,P.Y.SHI,A.CREANGA,A.PEGU,S.HANDLEY,D.WANG,A.BOON, REMARK 1 AUTH 4 J.E.CROWE,S.P.J.WHELAN,D.FREMONT,M.DIAMOND REMARK 1 TITL A POTENTLY NEUTRALIZING ANTI-SARS-COV-2 ANTIBODY INHIBITS REMARK 1 TITL 2 VARIANTS OF CONCERN BY BINDING A HIGHLY CONSERVED EPITOPE. REMARK 1 REF BIORXIV 2021 REMARK 1 REFN REMARK 1 PMID 33907753 REMARK 1 DOI 10.1101/2021.04.26.441501 REMARK 2 REMARK 2 RESOLUTION. 3.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.160 REMARK 3 NUMBER OF PARTICLES : 272007 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7MKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000256358. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SARS-COV-2 SPIKE BOUND BY SARS2 REMARK 245 -38 ANTIBODY FAB REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER H 7 OG1 THR H 21 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TRP A 353 170.08 -59.44 REMARK 500 ASN A 448 76.66 -104.84 REMARK 500 LEU A 517 66.59 -109.82 REMARK 500 LYS H 75 -1.70 83.00 REMARK 500 ASP H 103 47.54 -150.77 REMARK 500 TYR L 48 -164.14 -113.41 REMARK 500 SER L 51 19.96 58.96 REMARK 500 SER L 69 122.32 -170.16 REMARK 500 MET L 77 -142.82 57.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-23899 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-23898 RELATED DB: EMDB DBREF 7MKM A 333 520 UNP P0DTC2 SPIKE_SARS2 333 520 DBREF 7MKM H 1 113 PDB 7MKM 7MKM 1 113 DBREF 7MKM L 1 105 PDB 7MKM 7MKM 1 105 SEQRES 1 A 188 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 188 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 188 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 188 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 188 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 188 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 188 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 188 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 188 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 188 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 188 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 188 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 188 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 188 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 188 PHE GLU LEU LEU HIS ALA SEQRES 1 H 113 GLN VAL GLN LEU LYS GLU SER GLY PRO GLY LEU VAL ALA SEQRES 2 H 113 PRO SER GLN SER LEU SER ILE THR CYS THR VAL SER GLY SEQRES 3 H 113 PHE SER LEU THR ARG TYR GLY VAL HIS TRP VAL ARG GLN SEQRES 4 H 113 PRO PRO GLY LYS GLY LEU GLU TRP LEU GLY VAL ILE TRP SEQRES 5 H 113 ALA ASP GLY SER THR TYR TYR ASN SER ALA LEU MET SER SEQRES 6 H 113 ARG LEU SER ILE SER LYS ASP ASN SER LYS SER GLN VAL SEQRES 7 H 113 PHE LEU ASN MET ASN SER LEU GLN THR ASP ASP THR ALA SEQRES 8 H 113 LYS TYR TYR CYS ALA ARG ASP GLY ARG GLY TYR ASP ASP SEQRES 9 H 113 TYR TRP GLY GLN GLY THR THR LEU THR SEQRES 1 L 105 GLN ILE VAL LEU THR GLN SER PRO ALA ILE MET SER ALA SEQRES 2 L 105 SER PRO GLY GLU LYS VAL THR MET THR CYS SER ALA SER SEQRES 3 L 105 SER THR VAL SER PHE ILE TYR TRP TYR GLN GLN LYS PRO SEQRES 4 L 105 GLY SER SER PRO ARG LEU LEU ILE TYR ASP THR SER ASN SEQRES 5 L 105 PRO ALA SER GLY VAL PRO VAL ARG PHE SER GLY SER GLY SEQRES 6 L 105 CYS GLY THR SER TYR TYR LEU THR ILE SER ARG MET GLU SEQRES 7 L 105 ALA GLU ASP ALA ALA THR TYR TYR CYS GLN GLN TRP ASN SEQRES 8 L 105 THR TYR PRO LEU THR PHE GLY ALA GLY THR LYS LEU GLU SEQRES 9 L 105 LEU HET NAG A 601 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG C8 H15 N O6 HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 TYR A 365 ALA A 372 1 8 HELIX 3 AA3 GLY A 404 ILE A 410 1 7 HELIX 4 AA4 GLY A 416 ASN A 422 1 7 HELIX 5 AA5 SER H 84 ASP H 89 1 6 HELIX 6 AA6 TYR L 48 ASN L 52 5 5 HELIX 7 AA7 GLU L 78 ALA L 83 1 6 SHEET 1 AA1 5 ARG A 355 ILE A 358 0 SHEET 2 AA1 5 VAL A 395 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 SER A 514 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 CYS A 432 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 CYS A 379 -1 N LYS A 378 O VAL A 433 SHEET 1 AA2 2 LEU A 452 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA3 2 TYR A 473 GLN A 474 0 SHEET 2 AA3 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA4 4 GLN H 3 SER H 7 0 SHEET 2 AA4 4 LEU H 18 SER H 25 -1 O THR H 23 N LYS H 5 SHEET 3 AA4 4 GLN H 77 MET H 82 -1 O VAL H 78 N CYS H 22 SHEET 4 AA4 4 LYS H 71 ASP H 72 -1 N ASP H 72 O GLN H 77 SHEET 1 AA5 4 GLU H 46 LEU H 48 0 SHEET 2 AA5 4 GLY H 33 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 3 AA5 4 LYS H 92 ASP H 98 -1 O ALA H 96 N HIS H 35 SHEET 4 AA5 4 TYR H 105 THR H 110 -1 O GLY H 107 N CYS H 95 SHEET 1 AA6 4 VAL L 3 THR L 5 0 SHEET 2 AA6 4 VAL L 19 ALA L 25 -1 O SER L 24 N LEU L 4 SHEET 3 AA6 4 SER L 69 ILE L 74 -1 O TYR L 70 N CYS L 23 SHEET 4 AA6 4 SER L 62 CYS L 66 -1 N CYS L 66 O SER L 69 SHEET 1 AA7 3 LEU L 45 ILE L 47 0 SHEET 2 AA7 3 ILE L 32 GLN L 36 -1 N TRP L 34 O ILE L 47 SHEET 3 AA7 3 TYR L 85 GLN L 89 -1 O GLN L 88 N TYR L 33 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 480 CYS A 488 1555 1555 2.04 SSBOND 4 CYS H 22 CYS H 95 1555 1555 2.03 SSBOND 5 CYS L 23 CYS L 87 1555 1555 2.04 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.44 CISPEP 1 CYS A 336 PRO A 337 0 -14.20 CISPEP 2 TYR L 93 PRO L 94 0 -17.90 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000